Unification of the globally distributed spindle-shaped viruses of the Archaea

Abstract

Viruses with spindle-shaped virions are abundant in diverse environments. Over the years, such viruses have been isolated from a wide range of archaeal hosts. Evolutionary relationships between them remained enigmatic, however. Here, using structural proteins as markers, we define familial ties among these "dark horses" of the virosphere and segregate all spindle-shaped viruses into two distinct evolutionary lineages, corresponding to Bicaudaviridae and Fuselloviridae. Our results illuminate the utility of structure-based virus classification and bring additional order to the virosphere.

FIG 1

Negative-contrast electron micrographs of viral species with spindle-shaped virions. (A1) Three stages of extracellular tail development of ATV, the type species of the family Bicaudaviridae (35); (A2) STSV1 (27). (B1) SSV1, the type species of the genus Alphafusellovirus, family Fuselloviridae; (B2) Sulfolobus spindle-shaped virus 6 (SSV6), the type species of the genus Betafusellovirus, family Fuselloviridae (19); (B3) TPV1 (3); (B4), A3-VLP (25); (B5) PAV1 (2); (B6) APSV1 (26); (B7) His1 (20), the type species of the genus Salterprovirus. Scale bars, 100 nm.

FIG 2

Evolutionary relationship between spindle-shaped viruses with tails. (A) Genome maps of Acidianus two-tailed virus (ATV) and Sulfolobus tengchongensis spindle-shaped viruses 1 and 2 (STSV1 and -2). Homologous regions shared between STSV1 and STSV2 are connected by gray shading. Names of ATV genes that have homologs in STSV1 and/or STSV2 are indicated; the names of corresponding STSV1 and STSV2 genes are also shown. The new genus “Betabicaudavirus” within the family Bicaudaviridae is proposed for classification of STSV1 and STSV2. (B) Multiple alignment of major capsid protein sequences of ATV, STSV1, and STSV2. Note that products of ATV ORF145 and ORF131 are paralogs. GenBank identification (GI) numbers: ATV ORF131, 75750454; ATV ORF145, 75750440; STSV1 ORF40, 51980166; STSV2 gp37, 448260184. (C) Available X-ray structures of two ATV structural proteins, ORF131 (PDB ID no. 3FAJ) and ORF273 (PDB ID no. 4ATS), both displaying unique folds. Whereas a homologue of ORF131 is encoded by both STSV1 and STSV2 (A and B), ORF273 is unique to ATV.

FIG 3

Evolutionary relationship between tailless spindle-shaped viruses. (A) Multiple alignment of major capsid protein sequences. Red bars above the alignment denote the positions of the two hydrophobic α-helixes. The positively charged residues (R and K) found at the hydrophilic C-terminal tail following the hydrophobic domain are highlighted in red. GenBank identification (GI) numbers: SSV1 VP1, 19263455; ASV1 VP1, 270281782; His1 ORF21, 123827233; PAV1 ORF121, 125863384; TPV1 gp15, 378554458; A3-VLP Mvol0497, 297619025; APSV1 orf17-96, 371924949. (B) Hydrophobicity profiles of the capsid proteins aligned in panel A. (C) Pairwise identity and similarity (in parentheses) values calculated from the alignment shown in panel A using SIAS (http://imed.med.ucm.es/Tools/sias.html). Sequence similarity was calculated by taking into consideration the following physicochemical properties of aligned amino acids: aromatic (F, Y, W), hydrophobic (V, I, L, M, C, A, F, Y, W), aliphatic (V, I, L), positively charged (R, K, H), negatively charged (D, E), polar (N, Q, H, K, R, D, E, T, S), or small (A, T, S, G). The proposed taxonomic classification of the tailless spindle-shaped viruses is shown on the right.

FIG 4

An overlapping gene set shared by tailless spindle-shaped viruses. The diagram shows that in addition to the capsid protein (CP) gene, the viruses share an overlapping set of genes. The numbers next to the lines connecting the viruses denote the number of shared genes. PAV1, TPV1, and A3-VLP are proposed to be grouped into a new genus “Deltafusellovirus,” and are indicated with a triangle.